All software

Magic Castle

Magic Castle aims to recreate the HPC user experience in public clouds.

marzipan

Deploying clusters of VMs on bare metal using OpenNebula, provisioning, and running services made easy by fully configurable scalable automation

Mass Spec Studio for Clinical Proteomics

A fusion of the popular OpenMS suite of functionality with the powerful Mass Spec Studio. Users have access to OpenDIA and OpenPRM to support large scale processing of clinical proteomics data sets.

Medical Image Processing in Python

This lesson introduces some specifics of medical image processing with popular Python libraries such as SimpleITK, Pydicom and NiBabel. Reconstruction algorithms, image and DICOM anonymization, registration, segmentation, data augmentation and generative AI are covered.

mibibio

mibiremo

MiBiReMo (Microbiome Bioremediation Reaction Module) is a Python interface to the PhreeqcRM library. The package is designed to be coupled with transport models to simulate reactive transport in porous media, with applications in environmental and geochemical engineering.

mibiscreen

Data handling and screening package of the Microbiome based remediation Prediction Tool

mibitrans

A collection of analytical and semi-semianalytical solutions for hydrogeological transport phenomena

minimism

A minimal distributed MPI port from UFEMISM, used as a basis for UFEMISM2.0

MINTED

MINTED (Making Identifiers Necessary for Tracking Evolving Data) aims to apply dataset citation Digital Object Identifiers (DOIs) and researcher ORCIDs into ONC's Oceans 3.0 digital infrastructure.

Mixed Meal Model SBML

This software generates the SBML version of the Mixed Meal Model, for predicting the glucose level evolution after the intake of a meal.

MPET

This software is designed to run simulations of batteries with porous electrodes using porous electrode theory, which is a volume-averaged, multiscale approach to capture the coupled behavior of electrolyte and active material within electrodes

MSS-IMProv

An Integrative Modeling Platform

NanopubJL

JupyterLab extension to aid in searching and publishing of Nanopublications in a python notebook

Nature Counts

The NatureCounts platform allows users to collect, archive, interpret and access wildlife data to advance the understanding of bird populations across the Western Hemisphere.

nedextract

nedextract is a python library that helps you to extract information on person names and organisations mentioned in Dutch (annual report) PDF files.

NetCDF2LittleR

An application to convert NetCDF files to the Little-R format

NeuroAnalyzer

NeuroAnalyzer is a Julia toolbox for analyzing neurophysiological data.

NeuroGym

NeuroGym is a curated collection of neuroscience tasks with a common interface. The goal is to facilitate the training of neural network models on neuroscience tasks.

NPLinker

Microbial natural products data mining by integrating genomics and metabolomics data

NPLinker eScience Workshop GenMetMine Materials

These materials were used as a part of the NPLinker eScience Workshop on Natural Product Genome & Metabolome Mining: https://www.wur.nl/en/research-results/chair-groups/plant-sciences/bioinformatics/teaching/nplinker_workshop.htm Most materials are available in a format facilitating its reuse.

Nunaliit

The Nunaliit Atlas Framework aims to make it easy to tell stories and highlight relationships between many different forms of information from a variety of sources, using maps as a central way to connect and interact with the data.

OBiBa Agate

Agate is a web application that offers users related services to the OBiBa software stack.

OBiBa Mica

Mica is OBiBa's software application that is used to create data web portals for large-scale epidemiological studies or multiple-study consortia.

OBiBa Opal

Opal is OBiBa's core data repository application for epidemiological studies.

Ocean Networks Canada

By bringing data to the surface, ONC provides ocean intelligence to scientists, governments, organizations, and citizens. Ocean data are archived, processed and made freely available via ONC’s data management system, Oceans 3.0.

OCTSEG

Analyze retinal optical coherence tomography images.

One button compute

Web application for running a CWL workflow on a bunch of files.

OpenDA

Open data assimilation toolbox. OpenDA is an open interface standard for a set of tools to quickly implement data-assimilation and calibration for arbitrary numerical models.

OpenSim Creator

A UI for building OpenSim models

Orange3 Argument Mining Add-on

This open-source Python package facilitates the processing, analysis, and visualization of argument corpora. Additionally, It offers user-friendly GUIs integrated into the Orange3 scientific workflow platform, enabling non-programmers to utilize its capabilities.

Orange3 Story Navigator

Add-on providing quantitative textual story analysis based on principles in narrative psychology

Orange Hackathon

Orange modules for text processing in the project What Works When for Whom

Osmium

Start, stop and monitor applications remotely via a HTTP interface.

oTree Demo Experiments

oTree demo experiment: Public goods game

oTree Development Environment

A Docker environment for programming against multiple oTree server

oTree Waiting Room

A load balancer for oTree servers.

Overture Arranger

Data can be messy, let Arranger organize it for you.

Overture Data Management System

Overture is a collection of open-source, extendable solutions for big-data genomic science that research institutions and individual researchers can use to support their work.

Overture Ego

A stateless authorization and user management service.

Overture Maestro

Organizing your distributed data into one index.

Overture Score

Transfer data quickly and easily to and from any cloud-based storage system.

Overture Song

Quickly and reliably track genome metadata scattered across multiple Cloud storage systems.

PACTE

A Collaborative Electronic Text Annotation Platform

PanTools-pipeline-v4

General purpose Snakemake pipeline for PanTools v4.

paradigma

A toolbox to calculate digital biomarkers for wearable sensors in Parkinson's disease.

parareal

This package runs the parareal algorithm on a black-box simulator. Parallelisation is managed through Dask.

PattyAnalytics

Library for aligning and scaling one point cloud to an other.